Glacial meltwater discharge in fjords on the west coast of Spitsbergen is increasing due to climate change. The influence of this discharge on phytoplankton nutrient limitation, composition, productivity and photophysiology was investigated in central (M) and inner (G) Kongsfjorden (79°N, 11°40’E). Freshwater influx intensified stratification during June 2015, coinciding with surface nutrient depletion. Surface nutrient concentrations were negatively correlated with stratification strength at station M. Here, nitrate addition assays revealed increasing N limitation of surface phytoplankton during the second half of June, which was followed by a pronounced compositional change within the flagellate-dominated phytoplankton community as dictyochophytes (85% of chl a) were replaced with smaller haptophytes (up to 60% of chlorophyll a) and prasinophytes (20% of chlorophyll a). These changes were less pronounced at station G, where surface phosphate, ammonium and nitrate concentrations were occasionally higher, and correlated with wind direction, suggesting wind-mediated transport of nutrient-enriched waters to this inner location. Therefore, glacial meltwater discharge mediated nutrient enrichment in the inner fjord, and enhanced stratification in inner and central Kongsfjorden. Surface chlorophyll a and water column productivity showed 3–4-fold variability, and did not correlate with nutrient limitation, euphotic zone depth, or changed taxonomic composition. However, the maximum carbon fixation rate and photosynthetic efficiency showed weak positive correlations to prasinophyte, cryptophyte, and haptophyte chlorophyll a. The present study documented relationships between stratification, N limitation, and changed phytoplankton composition, but surface chlorophyll a concentration, phytoplankton photosynthetic characteristics, and water column productivity in Kongsfjorden appeared to be driven by mechanisms other than N limitation.